The complete chloroplast genome sequence of Lilium concolor var. pulchellum

Abstract Lilium concolor var. pulchellum is a perennial herbaceous plant with high ornamental and edible value; it is a critical breeding parent of Asiatic hybrids. In this study, we reported the complete chloroplast genome of L. concolor var. pulchellum. The total size of the genome is 152,126 bp with a GC content of 37.0%. It has a conserved quadripartite structure comprising 136 genes, including 38 tRNA genes, 8 rRNA genes, 83 protein-coding genes, and 7 pseudogenes. Phylogenetic analysis strongly supported a close relation between L. concolor var. pulchellum and L. callosum. The complete plastome sequence of L. concolor var. pulchellum could provide useful information for phyletic evolution of the genus Lilium.

Lilium concolor var. pulchellum (Fisch.) Regel 1876, belonging to the genus Lilium in the Liliaceae family, is an excellent germplasm resource of the genus Lilium. It has a great potential for development and utilization (Du et al. 2014). L. concolor var. pulchellum is naturally distributed in Northern China (Liaoning, Jilin, Heilongjiang, Hebei province), South Korea, Russia, and North Korea (Liang and Tamuram 2000). At present, the main phylogenetic clades of the genus Lilium have been basically defined, and the renewal system could be divided into seven sections (Martagon, Pseudolirium, Lilium, Archelirion, Sinomartagon, Leucolirion, and Oxypetalum) according to the morphological taxonomy and molecular phylogenetic methods (Gao et al. 2013;Du et al. 2017). Some of these groups are subdivided into several subgroups. Sinomartagon is the fifth group, divided into Sinomartagon5a and Sinomartagon5b due to morphological characteristics (Comber 1949;De 1974). In this study, we report the complete chloroplast (cp) genome of L. concolor var. pulchellum for the first time. It could provide the genomic resource for further studies on the genetic evolution of the genus Lilium.
Healthy and fresh leaves of L. concolor var. pulchellum species were collected from National Lily Germplasm Bank of Beijing Academy of Agriculture and Forestry Sciences, Beijing, China (39 56 0 37 00 N, 116 17 0 15 00 E). The collection of plant material was carried out in accordance with the guidelines provided by National Lily Germplasm Bank of Beijing Academy of Agriculture and Forestry Sciences and with the permission from the institution. The specimen was stored in the Herbarium, Institute of Botany, Chinese Academy of Sciences (contact Wang Zhongtao, pe@ibcas.ac.cn). The specimen accession number is Z0166. Total genomic DNA was extracted using a plant genome extraction kit (Tiangen, Beijing, China). Subsequently, DNA concentration was measured using a NanoDrop spectrophotometer 2000 (Thermo Fisher Scientific, America). DNA was sheared to construct a 400 bp (insert size) paired-end library by the Illumina HiSeq 4000 standard protocol. The paired-end reads were qualitatively assessed and completed using SPAdes 3.6.1 (Bankevich et al. 2012). The gaps were filled by PCR amplification and Sanger sequencing. The Sanger sequence reads were proofread and assembled with Sequencher 4.10 (http://www.genecodes.com).
To explore the phylogenetic relationship among this species and its related taxa, 17 Lilium chloroplast plastome sequences were downloaded from the NCBI Genbank database, using Cardiocrinum giganteum, Notholirion bulbuliferum, Notholirion campanulatum, and Fritillaria persica as the outgroup. Phylogenetic trees were constructed by the maximum-likelihood (ML) and Bayesian analysis (BI) methods using the entire cp genome. The ML analyses were performed using RAxML-HPC2 on XSEDE (8.2.12) at the CIPRES Science Gateway website (Stamatakis et al. 2008;Miller et al. 2015) (http://www.phylo.org/sub_sections/portal/), as suggested with 1000 bootstrap replicates. The BI was performed with MrBayes 3.2 (Ronquist et al. 2012). A random tree and 100,000 generations started in the Markov chain Monte Carlo (MCMC).
Phylogenetic analysis showed that L. concolor var. pulchellum belonged to Sinomartagon 5b, and it formed the closest clade with L. callosum with a strong bootstrap support of 100% (Figure 1). The chloroplast genome of L. concolor var. pulchellum provides the valuable genomic resource for the phylogenetic studies of the genus Lilium.

Disclosure statement
No potential conflict of interest was reported by the author(s).

Author contributions
Shengnan Kang was involved in the conception and design and analysis and interpretation of the data; Xuemin Zhang was involved in the drafting of the paper, Mingfang Zhang and Yunpeng Du were involved in revising it critically for intellectual content; Haiying Qin, Xiaonan Yu and Xiuhai Zhang were involved in the final approval of the version to be published; and that all authors agree to be accountable for all aspects of the work.

Data availability statement
This data has been uploaded to GenBank of NCBI at https://www.ncbi. nlm.nih.gov/genbank, with GenBank accession number MZ751064. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA791705, SRX13501476, and SAMN24338948, respectively.